RNA molecules are essential components of the cell and its primary structure dictates its folding. The function of the RNA is subsequently dictated by its structure. The overall structure of RNA molecules consists of small structural regions/domains that together build up the RNA structure. Consequently, small stable RNA structural regions/domains can be identified and be produced separately with a retained conformation as exemplified by Kufel and Kirsebom, 1998.
RNase P is a ribonucleoprotein complex present in all living cells (Altman and Kirsebom, 1999). It catalyses the removal of 5′ leader sequences from tRNA precursors and similar molecules. In bacteria, RNase P consists of one RNA subunit and a small basic protein, and it has been shown that the catalytic activity is associated with its RNA subunit. The RNA alone derived from bacteria is able to cleave a number of substrates correctly and efficiently in vitro in the absence of the protein (Guerrier-Takada et al., 1983). The reaction catalyzed by RNase P RNA alone as well as in the presence of the RNase P protein requires divalent metal ions such as Mg2+. It has been proposed that cleavage proceeds through a trigonal bipyramidal transition state (SN2), where two Mg2+ ions participate in the chemistry of the cleavage (Warnecke et al., 1996) defined as the two metal ion cleavage mechanism. In addition, Mg2+ ions are important for correct folding of RNase P RNA and for the interaction between RNase P and its substrate (Altman and Kirsebom, 1999).
The two metal ions cleavage mechanism is considered to be a general mechanism of catalysis in breakage and formation of phosphodiester bonds. Besides its importance in catalyzing RNA mediated cleavage of phosphodiester bonds it is well known that it is used by protein enzyme for the same purpose. The polymerizing and exonucleolytic activities of E. coli DNA polymerase I are the paradigm for two metal ion mediated catalysis (Steitz and Steitz, 1993). Other protein enzymatic activities proceeding through the two metal ion catalysis mechanism: a variety of prokaryotic and eukaryotic DNA polymerases, RNA polymerases, deoxyribo- and ribonucleases, phosphatases, kinases etc.
Several aminoglycosides are known to interact with RNA and interfere with its function. For example neomycin B interferes with protein biosynthesis due to binding to ribosomal RNA, inhibits the activity of several RNA based biocatalysts (known ribozymes) including RNase P RNA (Walter et al., 1999; Mikkelsen et al., 1999). The inhibitory effect caused by neomycin has been suggested to be due to displacement of essential divalent metal ions (Herrman and Westhof, J. Mol. Biol. vol. 276, 903-912, 1998). Direct evidence for displacement of a divalent metal has been obtained (Mikkelsen et al., 2001).